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- PDB-7z2t: Escherichia coli periplasmic phytase AppA D304A mutant, complex w... -

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Basic information

Entry
Database: PDB / ID: 7z2t
TitleEscherichia coli periplasmic phytase AppA D304A mutant, complex with myo-inositol hexakissulfate
ComponentsAcidphosphatase
KeywordsHYDROLASE / histidine acid phosphatase / phytase
Function / homology
Function and homology information


4-phytase / 4-phytase activity / acid phosphatase / acid phosphatase activity
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
D-MYO-INOSITOL-HEXASULPHATE / PHOSPHATE ION / Acidphosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsAcquistapace, I.M. / Brearley, C.A. / Hemmings, A.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M022978/1 United Kingdom
CitationJournal: Int J Mol Sci / Year: 2022
Title: Insights to the Structural Basis for the Stereospecificity of the Escherichia coli Phytase, AppA.
Authors: Acquistapace, I.M. / Thompson, E.J. / Kuhn, I. / Bedford, M.R. / Brearley, C.A. / Hemmings, A.M.
History
DepositionFeb 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acidphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8875
Polymers44,8441
Non-polymers1,0434
Water8,395466
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.490, 47.440, 65.560
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Acidphosphatase / AppA family phytase/histidine-type acid phosphatase / Bifunctional acid phosphatase/4-phytase / ...AppA family phytase/histidine-type acid phosphatase / Bifunctional acid phosphatase/4-phytase / Periplasmic AppA protein / Periplasmic AppA protein [includes: phosphoanhydrid phosphohydrolase and 4-phytase] / Phosphoanhydride phosphohydrolase (pH 2.5 acid phosphatase) (AP) / 4- phytase / Phosphoanhydride phosphorylase / Phytase AppA


Mass: 44843.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: appA, appA_1, appA_2, ABE90_015325, ACN81_22175, ACU57_13335, AM464_22895, AT845_000200, BANRA_01497, BANRA_01938, BANRA_04663, BGZ_00710, BJI68_21075, BJJ90_16615, BO068_002094, BON73_13465, ...Gene: appA, appA_1, appA_2, ABE90_015325, ACN81_22175, ACU57_13335, AM464_22895, AT845_000200, BANRA_01497, BANRA_01938, BANRA_04663, BGZ_00710, BJI68_21075, BJJ90_16615, BO068_002094, BON73_13465, BON74_03540, BON75_14340, BON77_16920, BON80_24545, BON89_12320, BON93_08495, BON97_03865, BON98_05845, BTQ06_12390, BvCmsHHP019_04940, BvCmsHHP056_02151, BvCmsKKP061_02619, BvCmsKSNP073_03019, C2U48_04610, C3F40_07155, C5N07_03615, C5Y87_10555, C9160_17160, CA593_23620, CG831_002343, COD53_24775, D0X26_04185, D3Y67_02885, D9D77_12200, DAH17_05470, DAH20_14220, DAH22_18875, DAH29_05070, DAH30_01065, DAH31_04130, DAH32_26115, DAH34_01475, DAH36_02680, DAH37_00935, DAH41_23775, DEN88_21760, DEN89_03775, DEN90_00590, DEN91_07910, DEN95_10355, DEO03_11685, DEO14_09085, DEO17_06365, DEO18_05115, DEO19_08440, DIV22_11465, DRW19_20065, DTL43_09820, DXT70_14350, DXT71_05565, DXT73_09385, E2119_16940, E2121_13515, E2131_21180, E2134_05840, E2135_21350, E4K51_09405, E5P22_02875, E5P23_07930, E5P26_11215, E5P27_02240, E5P28_01130, E5P29_00755, E5P31_05815, E5P32_09210, E5P33_05190, E5P35_09310, E5P36_09445, E5P40_03540, E5P51_06065, E5S36_05920, E5S42_07390, E5S51_10255, E5S57_04790, EAI46_03420, EC1094V2_2850, EC95NR1_05304, EIZ93_00240, ELT20_01855, ELT41_14085, ELX85_06365, ELY39_05280, ERS139208_02859, EYV17_08460, EYV18_02225, F2N31_24545, F9V24_04715, F9X20_13515, FDM60_03565, FOI11_008030, FOI11_12015, FQF29_10640, FV293_21365, G4A38_18295, G5632_05905, GKF89_10795, GKG12_05120, GP662_14105, GQE64_05300, GQM04_09625, GRW05_05690, GRW57_05130, GRW81_11950, HMV95_15325, HNC36_01680, HV209_06275, HVW19_24390, HVY77_16815, HX136_16165, I6H02_23730, IH768_04875, IH772_16025, J0541_003669, JNP96_09840, NCTC10958_03391, NCTC11181_00321, NCTC13216_03584, NCTC8008_02712, NCTC8960_00665, NCTC9037_03367, NCTC9706_00521, NCTC9962_02002, SAMEA3472044_00046, SAMEA3472067_00986, SAMEA3472080_00519, SAMEA3751407_00914, SAMEA3752557_01451, SAMEA3753106_00629, WP2S18E08_29460, WR15_11565
Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle Express T7 / References: UniProt: G0ZGJ8, 4-phytase, acid phosphatase

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Non-polymers , 5 types, 470 molecules

#2: Chemical ChemComp-IHS / D-MYO-INOSITOL-HEXASULPHATE


Mass: 660.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O24S6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES pH 6.5, 18 % w/v PEG 8000, 200 mM calcium acetate. Soaked in 20 % w/v PEG 3350, 9 mM IHS in 0.6 M glycine pH 3.0, 20 % glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.41→41.13 Å / Num. obs: 73471 / % possible obs: 99.17 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.08 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.047 / Net I/σ(I): 10.85
Reflection shellResolution: 1.41→1.46 Å / Mean I/σ(I) obs: 1.83 / Num. unique obs: 7274 / CC1/2: 0.494 / Rpim(I) all: 0.511

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DKL

1dkl


Resolution: 1.41→41.13 Å / SU ML: 0.1594 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2133
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.18 3692 5.03 %
Rwork0.1475 69778 -
obs0.1491 73470 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.78 Å2
Refinement stepCycle: LAST / Resolution: 1.41→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3109 0 59 466 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543270
X-RAY DIFFRACTIONf_angle_d0.84174481
X-RAY DIFFRACTIONf_chiral_restr0.0746515
X-RAY DIFFRACTIONf_plane_restr0.0074579
X-RAY DIFFRACTIONf_dihedral_angle_d11.0958476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.430.32611280.25522670X-RAY DIFFRACTION99.11
1.43-1.450.24781480.23362664X-RAY DIFFRACTION99.08
1.45-1.470.26451520.21292640X-RAY DIFFRACTION98.48
1.47-1.490.25311390.18962664X-RAY DIFFRACTION98.91
1.49-1.510.22571340.18552641X-RAY DIFFRACTION99.07
1.51-1.540.20841450.17362666X-RAY DIFFRACTION98.98
1.54-1.570.21751610.16322640X-RAY DIFFRACTION98.8
1.57-1.590.22341540.16462649X-RAY DIFFRACTION98.77
1.59-1.620.20331290.15612704X-RAY DIFFRACTION99.54
1.62-1.660.19831310.15382671X-RAY DIFFRACTION99.43
1.66-1.690.19721650.15172689X-RAY DIFFRACTION99.72
1.69-1.730.22121650.14562636X-RAY DIFFRACTION99.82
1.73-1.780.16941430.14572682X-RAY DIFFRACTION99.61
1.78-1.820.22641450.1432724X-RAY DIFFRACTION99.76
1.82-1.880.16081390.1372691X-RAY DIFFRACTION99.68
1.88-1.940.16341340.13262680X-RAY DIFFRACTION99.43
1.94-2.010.1751450.13652669X-RAY DIFFRACTION99.54
2.01-2.090.15641440.13472698X-RAY DIFFRACTION99.54
2.09-2.180.16821340.13282696X-RAY DIFFRACTION99.26
2.18-2.30.17431420.12912687X-RAY DIFFRACTION99.02
2.3-2.440.1781140.13442726X-RAY DIFFRACTION99.54
2.44-2.630.15741530.14312702X-RAY DIFFRACTION99.34
2.63-2.90.17891090.15112732X-RAY DIFFRACTION99.37
2.9-3.310.17361300.14032725X-RAY DIFFRACTION98.96
3.32-4.170.1521340.13592704X-RAY DIFFRACTION98.44
4.18-100.16321750.15292728X-RAY DIFFRACTION97.55

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